AIMC Topic: Computational Biology

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Research on drug-drug interaction prediction using capsule neural network based on self-attention mechanism.

BMC bioinformatics
BACKGROUND: Multi-drug combinations represent an effective strategy for treating complex diseases. However, due to the vast number of unknown interactions among drugs, accurately predicting drug-drug interactions (DDIs) is essential for preventing ad...

Multi-omics driven computational framework for cancer molecular subtype classification.

Scientific reports
Cancer molecular subtype classification is an essential component of precision oncology which provides insights into cancer prognosis and guides targeted therapy. Despite the growing applications of AI for cancer molecular subtype classification, cha...

BGC-MAC and BGC-MAP: Attention-Based Models for Biosynthetic Gene Cluster Classification and Product Matching.

Journal of chemical information and modeling
Natural products, synthesized via enzymes encoded by biosynthetic gene clusters (BGCs), represent a major source of therapeutic agents. Accurate BGC annotation is essential to unlocking the vast potential of natural product diversity. However, BGC an...

Revealing the anti-tumor mechanisms of aromatic oil from Amomum villosum through integrated network pharmacology, bioinformatics, machine learning, single-cell sequencing, and cell experiments.

Biochemical and biophysical research communications
The dry fruits of Amomum villosum (Av) are a traditional Chinese medicine used for gastrointestinal disease. Aromatic oil has been reported to have anti-tumor properties. However, its therapeutic potential and molecular mechanisms remain unclear. Int...

Exploring shared diagnostic genes and molecular mechanisms in multiple sclerosis and psoriasis through bioinformatics analysis and machine learning.

Biochemical and biophysical research communications
BACKGROUND: Multiple sclerosis (MS) and psoriasis are both immune-mediated inflammatory diseases. Previous studies have reported comorbidity between MS and psoriasis, but the underlying mechanisms remain unclear. This study aims to elucidate the shar...

Exploring the mechanism of autophagy and inflammation in osteoarthritis through bioinformatics and experimental verification.

Autoimmunity
Osteoarthritis (OA) is a chronic joint disorder characterized by cartilage degradation and accompanied by inflammatory processes. Inflammation and autophagy dysfunction have been associated with the pathogenesis of OA. However, the interplay between ...

Feature learning augmented with sampling and heuristics (FLASH) improves model performance and biomarker identification.

NPJ systems biology and applications
Big biological datasets, such as gene expression profiles, often contain redundant features that degrade model performance and limit generalization across independent datasets with complexities like class imbalance and hidden sub-clusters. To overcom...

Prompt-CBP: A Novel Prompt Learning-Based Model for Predicting Cross-Species Promoters.

Journal of chemical information and modeling
Promoter sequences across species exhibit both specificity and conservation. The specificity of promoter sequences typically leads to lower cross-species prediction performance compared to within-species prediction. However, conserved promoter motifs...

AttMVGraph: Attention-Based Multimodal Fusion and Variational Graph Learning for SM-miRNA Association Prediction.

Journal of chemical information and modeling
MiRNA serves as a key noncoding RNA regulating gene expression and is frequently targeted as a therapeutic small molecule (SM). However, relying solely on the experimental identification of SM-miRNA interactions proves costly and inefficient. To addr...

AcidProNet: Acidophilic Protein Classification via DCGAN-GP-Based Data Augmentation and Parameter-Shared Mixture-of-Experts Transformer.

Journal of chemical information and modeling
With the continued exploration of biological resources in extreme environments, functional proteins such as acidophilic proteins have attracted increasing attention. These proteins can maintain structural stability and biological functionality under ...